The quality shown in the armory is for the pet item
, not the quality of the pet itself. Wild pets will show up on the armory as the same quality in your Pet Journal because there's no item that "teaches" you the companion. But any pet that requires an item to learn it will only show the item quality on the armory.
Example: Magical Crawdad
(pet) = rare qualityMagical Crawdad Box
(item) = common (white) quality
The item quality and pet quality sometimes don't match up. You could find a blue pet item, learn it, but then find out the new companion is only uncommon in your Pet Journal. An example of this inconsistency is the Darkmoon Rabbit. The item that teaches you the rabbit is epic, but the rabbit itself is only rare quality.